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Finding list of parameters available

For the nf-core pipelines, the tools implemented and the range of parameters available are generally described in the Usage section. Some of the parameters will be required, others optional.

 

Let’s have a look at the nf-core/rnaseq pipeline:

All the parameters available will also be listed under the Parameters section:

Exercise 1

Using the usage and parameters sections, search how many aligner options are available for the nf-core rnaseq pipeline version 3.15.1.

 Solution

There are 3 aligner algorithms available: 'star_salmon', 'star_rsem' and 'hisat2'. Star_salmon is the one that is run by default.

Specifying parameters on the command line

Parameters are generally specified on the CLI (i.e. command line interface).

nextflow run nf-core/rnaseq -profile singularity -resume \
        --input samplesheet.csv \
        --outdir results \
        --genome GRCm38 \
        --aligner star_salmon \
        --extra_trimgalore_args "--quality 30 --clip_r1 10 --clip_r2 10 --three_prime_clip_r1 1 --three_prime_clip_r2 1 "

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